The 2003 Owner Benefits guide states that when warranty service is being done, "alternate transportation will be provided for you." "Alternate transporation" can mean several things, including loaner car, shuttle service, or rental car. Now, that said, it may be that no loaners were available when you brought the car in, but they should have put you into a rental at the very least. If you were not offered or provided one of these alternate transportation options, I'd definitely ask about it. For me, this is part of why I chose a Lincoln in the first place. If your dealer gives you lip service, call the Lincoln Customer Service line at 1-800-521-4140.
Also, since you're so close to the end, I'd make darn sure your car is under factory warranty. According to the warranty guide, the warranty start date is the date you take delivery or the first day it is put into service (e.g., as a dealer demonstrator), whichever occurs first. End date is 4 years after the start date or 50K miles, whichever occurs first.
Good Luck.